Mutagenetix > Incidental Mutation

Incidental Mutation 'R1913:Vars2'

214627

Institutional Source

Beutler Lab

Gene Symbol

Vars2

Ensembl Gene

ENSMUSG00000038838

Gene Name

valyl-tRNA synthetase 2, mitochondrial

Synonyms

Vars2l, 1190004I24Rik

MMRRC Submission

039931-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R1913 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

35966526-35978484 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 35977814 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Proline to Serine at position 69 (P69S)

Ref Sequence

ENSEMBL: ENSMUSP00000047917 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000001565] [ENSMUST00000043674] [ENSMUST00000160039] [ENSMUST00000160734] [ENSMUST00000160752] [ENSMUST00000165144] [ENSMUST00000162266] [ENSMUST00000169093]

AlphaFold

Q3U2A8

Predicted Effect

probably benign
Transcript: ENSMUST00000001565

SMART Domains

Protein: ENSMUSP00000001565
Gene: ENSMUSG00000001524

Domain	Start	End	E-Value	Type
Pfam:Tfb2	22	375	6.4e-141	PFAM
PDB:3DOM\|C	383	459	7e-13	PDB

Predicted Effect

probably benign
Transcript: ENSMUST00000043674
AA Change: P69S

PolyPhen 2 Score 0.022 (Sensitivity: 0.95; Specificity: 0.81)

SMART Domains

Protein: ENSMUSP00000047917
Gene: ENSMUSG00000038838
AA Change: P69S

Domain	Start	End	E-Value	Type
Pfam:tRNA-synt_1	112	736	3.3e-179	PFAM
Pfam:tRNA-synt_1g	141	221	2e-8	PFAM
Pfam:Anticodon_1	780	932	3.6e-32	PFAM
low complexity region	1005	1015	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000159671

Predicted Effect

probably benign
Transcript: ENSMUST00000160039

SMART Domains

Protein: ENSMUSP00000124683
Gene: ENSMUSG00000001524

Domain	Start	End	E-Value	Type
Pfam:Tfb2	22	164	2.9e-44	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000160535

Predicted Effect

probably benign
Transcript: ENSMUST00000160734

SMART Domains

Protein: ENSMUSP00000124335
Gene: ENSMUSG00000001524

Domain	Start	End	E-Value	Type
Pfam:Tfb2	22	375	1.9e-137	PFAM
PDB:3DOM\|C	383	459	7e-13	PDB

Predicted Effect

probably benign
Transcript: ENSMUST00000160752

SMART Domains

Protein: ENSMUSP00000124458
Gene: ENSMUSG00000001524

Domain	Start	End	E-Value	Type
Pfam:Tfb2	22	160	6.4e-32	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000165144
AA Change: T71I

PolyPhen 2 Score 0.013 (Sensitivity: 0.96; Specificity: 0.78)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000162894

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000162927

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000171536

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000165787

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000162604

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000164978

Predicted Effect

probably benign
Transcript: ENSMUST00000168922

SMART Domains

Protein: ENSMUSP00000129196
Gene: ENSMUSG00000038838

Domain	Start	End	E-Value	Type
Pfam:tRNA-synt_1	2	386	3e-105	PFAM
Pfam:Anticodon_1	430	566	8.2e-29	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000162266

SMART Domains

Protein: ENSMUSP00000124103
Gene: ENSMUSG00000001524

Domain	Start	End	E-Value	Type
Pfam:Tfb2	22	91	1.8e-22	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000169093

SMART Domains

Protein: ENSMUSP00000126794
Gene: ENSMUSG00000038838

Domain	Start	End	E-Value	Type
Pfam:tRNA-synt_1	1	109	1.7e-29	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000164404

SMART Domains

Protein: ENSMUSP00000126084
Gene: ENSMUSG00000038838

Domain	Start	End	E-Value	Type
Pfam:tRNA-synt_1	1	201	1e-49	PFAM
Pfam:tRNA-synt_1g	68	172	4e-7	PFAM

Coding Region Coverage

1x: 97.5%
3x: 97.0%
10x: 95.6%
20x: 93.4%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a mitochondrial aminoacyl-tRNA synthetase, which catalyzes the attachment of valine to tRNA(Val) for mitochondrial translation. Mutations in this gene cause combined oxidative phosphorylation deficiency-20, and are also associated with early-onset mitochondrial encephalopathies. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Aug 2014]

Allele List at MGI

Other mutations in this stock

Total: 105 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca16	A	T	7: 120,140,463 (GRCm39)	I1588F	probably benign	Het
Abcc2	A	T	19: 43,795,683 (GRCm39)	T480S	probably benign	Het
Acnat1	A	G	4: 49,447,498 (GRCm39)	I361T	probably damaging	Het
Adamts10	A	T	17: 33,768,529 (GRCm39)	H869L	probably benign	Het
Agpat5	T	C	8: 18,929,629 (GRCm39)	C253R	probably benign	Het
Agtrap	T	A	4: 148,168,434 (GRCm39)	H15L	probably damaging	Het
Ahnak	T	A	19: 8,985,286 (GRCm39)	V2190E	probably damaging	Het
Alx4	A	G	2: 93,505,732 (GRCm39)	E278G	probably damaging	Het
Amz2	T	C	11: 109,319,697 (GRCm39)	S28P	probably damaging	Het
Atr	T	A	9: 95,748,786 (GRCm39)	Y444N	probably benign	Het
Brdt	T	C	5: 107,496,479 (GRCm39)	I197T	probably benign	Het
Ccser1	G	T	6: 62,356,878 (GRCm39)	S772I	probably damaging	Het
Cdh16	T	C	8: 105,343,100 (GRCm39)	H657R	probably benign	Het
Ceacam5	A	T	7: 17,493,502 (GRCm39)	K842*	probably null	Het
Cep120	G	A	18: 53,856,358 (GRCm39)	T353I	probably benign	Het
Chrnb1	T	C	11: 69,684,410 (GRCm39)	N164S	possibly damaging	Het
Cse1l	T	C	2: 166,764,111 (GRCm39)	F123L	probably damaging	Het
Cul7	T	A	17: 46,974,116 (GRCm39)	L1467H	probably damaging	Het
Dcx	G	C	X: 142,706,099 (GRCm39)	L231V	probably damaging	Het
Dnah12	T	C	14: 26,514,221 (GRCm39)		probably null	Het
Dnah2	A	T	11: 69,355,756 (GRCm39)	M2227K	probably damaging	Het
Dnajc30	G	A	5: 135,093,186 (GRCm39)	A28T	probably benign	Het
Dnm1l	T	C	16: 16,147,830 (GRCm39)	T306A	probably benign	Het
Elapor2	T	G	5: 9,316,275 (GRCm39)	L2R	probably damaging	Het
Enpp3	C	A	10: 24,652,669 (GRCm39)	E763*	probably null	Het
Esyt3	T	C	9: 99,202,364 (GRCm39)	S516G	probably benign	Het
Exoc3	T	C	13: 74,330,435 (GRCm39)	Q498R	probably damaging	Het
Fbn2	T	A	18: 58,194,814 (GRCm39)	N1449I	probably damaging	Het
Fgb	T	C	3: 82,952,287 (GRCm39)	D194G	probably benign	Het
Fgd3	T	C	13: 49,417,324 (GRCm39)	D713G	possibly damaging	Het
Foxb1	T	A	9: 69,667,383 (GRCm39)	Y49F	possibly damaging	Het
Fpr3	A	G	17: 18,191,670 (GRCm39)	I314V	probably damaging	Het
Gfod1	A	T	13: 43,456,921 (GRCm39)	I18N	probably damaging	Het
Gm5407	T	C	16: 49,117,283 (GRCm39)		noncoding transcript	Het
Gpr89	A	G	3: 96,782,949 (GRCm39)	F334L	possibly damaging	Het
Gucy2d	G	T	7: 98,093,054 (GRCm39)	V144F	probably benign	Het
H2-M10.5	C	A	17: 37,085,660 (GRCm39)	P273H	probably damaging	Het
H2-T13	T	A	17: 36,391,908 (GRCm39)	K237M	probably damaging	Het
Hcn2	A	G	10: 79,566,777 (GRCm39)	M485V	probably benign	Het
Helz2	G	T	2: 180,875,543 (GRCm39)	S1650R	probably damaging	Het
Ifnar2	T	C	16: 91,201,058 (GRCm39)	V433A	probably benign	Het
Igsf21	T	A	4: 139,834,623 (GRCm39)	Y83F	probably benign	Het
Kcnk18	A	G	19: 59,223,490 (GRCm39)	I212V	possibly damaging	Het
Kcns2	T	C	15: 34,839,855 (GRCm39)	I406T	probably damaging	Het
Krt42	C	T	11: 100,158,075 (GRCm39)	V166M	possibly damaging	Het
Lama3	T	C	18: 12,628,336 (GRCm39)	M1476T	probably benign	Het
Lcor	A	G	19: 41,546,913 (GRCm39)	R166G	probably benign	Het
Mapt	C	T	11: 104,218,901 (GRCm39)	P354L	probably damaging	Het
Mep1b	A	T	18: 21,226,286 (GRCm39)	I383F	probably benign	Het
Mpzl1	C	A	1: 165,429,374 (GRCm39)	C222F	probably benign	Het
Mug2	T	C	6: 122,047,829 (GRCm39)	L780P	probably damaging	Het
Naip2	C	T	13: 100,288,665 (GRCm39)		probably null	Het
Ndufab1	T	C	7: 121,695,914 (GRCm39)	D41G	probably benign	Het
Ntn1	A	G	11: 68,104,011 (GRCm39)	C546R	probably damaging	Het
Or2a5	T	A	6: 42,873,687 (GRCm39)	F101I	probably damaging	Het
Pakap	A	G	4: 57,892,963 (GRCm39)	E880G	probably damaging	Het
Pde6b	A	G	5: 108,575,056 (GRCm39)	E639G	probably benign	Het
Phf10	T	C	17: 15,177,071 (GRCm39)	T83A	probably benign	Het
Phkb	T	A	8: 86,628,549 (GRCm39)	I186N	possibly damaging	Het
Pkhd1	A	G	1: 20,636,980 (GRCm39)		probably null	Het
Plxnd1	C	A	6: 115,954,978 (GRCm39)	A595S	possibly damaging	Het
Ppara	T	A	15: 85,685,300 (GRCm39)	H416Q	probably damaging	Het
Prodh	T	A	16: 17,898,891 (GRCm39)	D188V	probably damaging	Het
Psmd14	A	T	2: 61,615,800 (GRCm39)	K223M	possibly damaging	Het
Ptpn5	A	G	7: 46,728,616 (GRCm39)	M528T	possibly damaging	Het
Rassf9	G	A	10: 102,380,800 (GRCm39)	E59K	probably benign	Het
Rnf2	A	T	1: 151,351,936 (GRCm39)	L140H	probably damaging	Het
Scai	A	G	2: 38,970,093 (GRCm39)	F557S	probably damaging	Het
Sdk2	A	G	11: 113,747,552 (GRCm39)	S653P	possibly damaging	Het
Sec24c	A	G	14: 20,739,179 (GRCm39)	D534G	probably benign	Het
Semp2l2a	T	A	8: 13,887,143 (GRCm39)	Q316L	probably benign	Het
Septin4	T	C	11: 87,457,838 (GRCm39)	S71P	probably benign	Het
Serinc1	A	G	10: 57,395,561 (GRCm39)	V375A	probably benign	Het
Serpinb9f	C	T	13: 33,509,829 (GRCm39)	A7V	probably damaging	Het
Smco1	T	C	16: 32,092,700 (GRCm39)	S124P	probably damaging	Het
Smim23	C	A	11: 32,774,441 (GRCm39)	C26F	possibly damaging	Het
Sppl2c	T	A	11: 104,078,715 (GRCm39)	M505K	probably benign	Het
Sprr1b	C	A	3: 92,344,775 (GRCm39)	V34F	possibly damaging	Het
Sun1	G	A	5: 139,221,487 (GRCm39)		probably null	Het
Supt16	A	G	14: 52,415,592 (GRCm39)	L381P	possibly damaging	Het
Syne2	A	G	12: 75,946,020 (GRCm39)	D364G	possibly damaging	Het
Tax1bp1	G	T	6: 52,742,937 (GRCm39)	V775F	probably damaging	Het
Tial1	T	A	7: 128,046,383 (GRCm39)	I231F	probably damaging	Het
Tiam1	C	A	16: 89,595,582 (GRCm39)	V1300L	probably damaging	Het
Tmem132e	A	G	11: 82,334,243 (GRCm39)	T585A	probably damaging	Het
Tnni3k	C	T	3: 154,684,836 (GRCm39)	A165T	probably benign	Het
Tomm40	A	T	7: 19,444,886 (GRCm39)	I165N	probably damaging	Het
Tomt	T	C	7: 101,550,454 (GRCm39)	E104G	probably damaging	Het
Topaz1	T	C	9: 122,596,078 (GRCm39)	S950P	possibly damaging	Het
Traf3ip2	C	G	10: 39,501,936 (GRCm39)	P28R	probably benign	Het
Trim24	C	T	6: 37,934,750 (GRCm39)	P822S	probably damaging	Het
Upf3a	T	G	8: 13,842,108 (GRCm39)	Y175D	probably damaging	Het
Veph1	T	C	3: 66,151,976 (GRCm39)	Y151C	probably damaging	Het
Vmn2r11	T	A	5: 109,202,654 (GRCm39)	D141V	probably benign	Het
Vwa5b1	G	A	4: 138,319,331 (GRCm39)	Q442*	probably null	Het
Wdr17	T	A	8: 55,140,761 (GRCm39)	D197V	probably damaging	Het
Wdr70	G	T	15: 7,913,891 (GRCm39)	T586N	possibly damaging	Het
Wfdc18	G	A	11: 83,600,754 (GRCm39)	G52R	probably benign	Het
Zc3h6	T	C	2: 128,858,540 (GRCm39)	I857T	probably damaging	Het
Zfp318	GAAGAA	GAAGAACAAGAA	17: 46,723,450 (GRCm39)		probably benign	Het
Zfp318	TGAAGAAGAAGAAGAAGAAGAAGAAGAAG	TGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAG	17: 46,723,440 (GRCm39)		probably benign	Het
Zfp647	C	T	15: 76,796,151 (GRCm39)	V170I	probably benign	Het
Zfp871	T	C	17: 32,994,891 (GRCm39)	N76D	possibly damaging	Het
Zpld2	A	G	4: 133,919,986 (GRCm39)		probably null	Het
Zwilch	A	G	9: 64,068,234 (GRCm39)	Y194H	probably damaging	Het

Other mutations in Vars2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02106:Vars2	APN	17	35,975,513 (GRCm39)	unclassified	probably benign
IGL02320:Vars2	APN	17	35,971,346 (GRCm39)	missense	probably benign	0.07
IGL02580:Vars2	APN	17	35,971,777 (GRCm39)	missense	possibly damaging	0.50
IGL02691:Vars2	APN	17	35,971,140 (GRCm39)	missense	probably damaging	1.00
IGL03039:Vars2	APN	17	35,975,013 (GRCm39)	missense	probably damaging	1.00
PIT4445001:Vars2	UTSW	17	35,977,103 (GRCm39)	nonsense	probably null
R0079:Vars2	UTSW	17	35,970,048 (GRCm39)	missense	probably damaging	0.99
R0152:Vars2	UTSW	17	35,970,919 (GRCm39)	missense	probably damaging	1.00
R0346:Vars2	UTSW	17	35,975,756 (GRCm39)	unclassified	probably benign
R0426:Vars2	UTSW	17	35,975,476 (GRCm39)	missense	probably damaging	1.00
R0584:Vars2	UTSW	17	35,977,578 (GRCm39)	missense	possibly damaging	0.82
R0589:Vars2	UTSW	17	35,970,068 (GRCm39)	missense	probably benign
R0882:Vars2	UTSW	17	35,968,191 (GRCm39)	missense	probably benign	0.41
R1234:Vars2	UTSW	17	35,978,038 (GRCm39)	missense	probably damaging	1.00
R1263:Vars2	UTSW	17	35,972,501 (GRCm39)	missense	probably damaging	1.00
R1559:Vars2	UTSW	17	35,977,150 (GRCm39)	unclassified	probably benign
R1772:Vars2	UTSW	17	35,970,976 (GRCm39)	missense	probably damaging	1.00
R1809:Vars2	UTSW	17	35,973,108 (GRCm39)	missense	probably damaging	1.00
R1986:Vars2	UTSW	17	35,970,953 (GRCm39)	missense	probably damaging	1.00
R2504:Vars2	UTSW	17	35,975,685 (GRCm39)	missense	probably damaging	1.00
R3426:Vars2	UTSW	17	35,972,866 (GRCm39)	missense	probably damaging	1.00
R4539:Vars2	UTSW	17	35,977,780 (GRCm39)	missense	probably damaging	0.99
R4751:Vars2	UTSW	17	35,970,235 (GRCm39)	missense	possibly damaging	0.89
R4861:Vars2	UTSW	17	35,972,825 (GRCm39)	missense	probably benign	0.00
R4861:Vars2	UTSW	17	35,972,825 (GRCm39)	missense	probably benign	0.00
R5028:Vars2	UTSW	17	35,970,365 (GRCm39)	critical splice donor site	probably null
R5217:Vars2	UTSW	17	35,969,041 (GRCm39)	missense	probably damaging	1.00
R5292:Vars2	UTSW	17	35,971,678 (GRCm39)	missense	probably damaging	1.00
R6056:Vars2	UTSW	17	35,976,680 (GRCm39)	missense	probably benign	0.01
R6211:Vars2	UTSW	17	35,976,554 (GRCm39)	splice site	probably null
R6213:Vars2	UTSW	17	35,971,332 (GRCm39)	missense	probably benign	0.27
R6374:Vars2	UTSW	17	35,970,937 (GRCm39)	missense	probably damaging	1.00
R6746:Vars2	UTSW	17	35,971,294 (GRCm39)	critical splice donor site	probably null
R6749:Vars2	UTSW	17	35,977,605 (GRCm39)	missense	probably damaging	1.00
R6957:Vars2	UTSW	17	35,977,967 (GRCm39)	missense	probably benign	0.39
R7107:Vars2	UTSW	17	35,969,142 (GRCm39)	missense	probably damaging	1.00
R7428:Vars2	UTSW	17	35,977,578 (GRCm39)	missense	probably benign	0.00
R7538:Vars2	UTSW	17	35,971,672 (GRCm39)	missense	probably damaging	1.00
R7553:Vars2	UTSW	17	35,975,680 (GRCm39)	missense	possibly damaging	0.93
R7741:Vars2	UTSW	17	35,971,835 (GRCm39)	missense	probably damaging	1.00
R7784:Vars2	UTSW	17	35,969,050 (GRCm39)	missense	possibly damaging	0.95
R7823:Vars2	UTSW	17	35,970,028 (GRCm39)	missense	probably damaging	1.00
R7915:Vars2	UTSW	17	35,975,731 (GRCm39)	missense	probably damaging	1.00
R8201:Vars2	UTSW	17	35,969,202 (GRCm39)	missense	probably benign
R8955:Vars2	UTSW	17	35,972,541 (GRCm39)	missense	probably damaging	1.00
R8964:Vars2	UTSW	17	35,970,699 (GRCm39)	missense	possibly damaging	0.46
R9101:Vars2	UTSW	17	35,969,980 (GRCm39)	missense	possibly damaging	0.51
R9202:Vars2	UTSW	17	35,977,551 (GRCm39)	missense	probably damaging	1.00
R9202:Vars2	UTSW	17	35,974,444 (GRCm39)	critical splice acceptor site	probably null
R9450:Vars2	UTSW	17	35,973,027 (GRCm39)	missense	probably damaging	0.98
X0021:Vars2	UTSW	17	35,969,926 (GRCm39)	missense	possibly damaging	0.93
Z1176:Vars2	UTSW	17	35,975,683 (GRCm39)	missense	possibly damaging	0.55
Z1177:Vars2	UTSW	17	35,974,364 (GRCm39)	missense	probably benign	0.17

Predicted Primers

PCR Primer
(F):5'- CCAGAAACATCTGTGGAAGCAG -3'
(R):5'- CACTTTGTACACAGCCGGAG -3'

Sequencing Primer
(F):5'- GAACAGAGATCCACTACTGAACTG -3'
(R):5'- TCCCCTGTCTCTCGGAGGAAC -3'

Posted On

2014-07-14